A prospective study was conducted to monitor the pig population in Iowa for the emergence of new subtype(s) of swine influenza virus (SIV) other than classic H1N1 subtype. During the study, an apparently new subtype of SIV, H3N2, was isolated in association with severe reproductive and respiratory clinical disease in swine operations in Iowa and southern Minnesota. At the same time, influenza outbreaks of this subtype also were reported in other states such as North Carolina, Illinois, and Texas. To date, the new subtype of SIV has been determined to be widely spread in swine operations throughout Iowa and is expected to coexist with H1N1 subtype in swine populations in the United States. A serological survey on 6-month-old finishing pigs (N=1064) from 129 herds throughout 29 counties in Iowa demonstrated that 64% of the pigs and 92.2% of the herds had serological evidence of exposure to H3N2 SIV as of June, 1999. The isolation of H3N2 subtype SIV in association with severe clinical disease brings a new perspective to the diagnosis and control of swine influenza in this country. New vaccines will be needed for effective control of H3N2 because field reports have indicated no cross protection against H3N2 subtype SIV by vaccines currently available for H1N1 strains. Consequently it is critical for diagnosticians to have rapid and accurate methods for the diagnosis and differentiation of SIV subtypes so that effective control measure can be suggested in timely manner.